VAV1 p.Pro119=
c.357G>A · rs373664582 · VCV1640649
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.138%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.6 | GERP -3.3 |
| Overall | ||
| CADD | 3.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.138%
East Asian · 62/44,870 alleles
Filtering AF
0.111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.101%
Overall
0.00843%
136/1,614,124 alleles · rare
exomes 110/1,461,872 · genomes 26/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.138% | 724 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,125 |
| South Asian | 0.0176% | 5,693 |
| African / African-American | 0.004% | 25,008 |
| European (non-Finnish) | 0.00297% | 33,715 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- VAV1
- Protein
- p.Pro119=
- Coding
- c.357G>A
- MANE Select
- NM_005428
- dbSNP
- rs373664582
- Type
- single nucleotide variant
- Location
- chr19:6821657 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.63 · 10 PDB
- Residue 119
- the calponin-homology (ch) domain; an α-helix
Similar variants
- VAV1 p.Pro119Leu Uncertain significance ★ ⚠ same residue
- VAV1 p.Ala168Val Uncertain significance ★★ ⚠ same type
- VAV1 p.Ala362Thr Uncertain significance ★★ ⚠ same type
- VAV1 p.Ala734Thr Uncertain significance ★★ same type
- VAV1 p.Arg15Gln Uncertain significance ★★ ⚠ same type
- VAV1 p.Arg179Ser Uncertain significance ★★ ⚠ same type
- VAV1 p.Arg195His Uncertain significance ★★ ⚠ same type
- VAV1 p.Arg282His Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/vav1-p-pro119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown